GSTR-9: Late Fee Slabs and the Three-Year Bar

GSTR explained: this guide covers what it means, who it applies to, the step-by-step process, documents required, fees, due dates and penalties in India — so you can stay compliant with confidence and avoid costly mistakes.

Late filing of an annual return used to cost the same regardless of size — ₹200 a day for everyone. Notification No. 07/2023 replaced that with three turnover slabs. But the more consequential change came from the Finance Act, 2023, which for the first time made it impossible to file at all after three years.

Section 47(2) levies a late fee of ₹100 per day for delay in furnishing GSTR-9, "subject to a maximum amount of quarter percent (0.25%) of the turnover in the State or Union Territory" — mirrored under the SGST/UTGST Act, so ₹200 a day capped at 0.5% in total. Notification No. 07/2023-Central Tax dated 31.03.2023 rationalised this into three turnover slabs from FY 2022-23 onwards. And section 44(2), inserted by the Finance Act, 2023 effective 01.10.2023, bars filing "after the expiry of a period of three years from the due date."

The three slabs, from FY 2022-23

Note that the cap moves far more than the daily rate. Between the second and third slab the daily fee doubles, but the ceiling multiplies twelve and a half times — from 0.02% to 0.25%. For a large taxpayer, the cap is the operative number.

And read both columns per Act. A ₹30 crore taxpayer accrues ₹200 a day in total, capped at 0.5% of State turnover across CGST and SGST together.

The one-time waiver that has closed

"The late fees in excess of ₹20,000 (₹10,000 CGST + ₹10,000 SGST/UTGST) shall be waived, for those registered persons who fail to furnish the annual return for FY 2017-18, 2018-19, 2019-20, 2020-21 and 2021-22 by the due date, if the annual return is furnished by 31st August 2023" — Notification No. 7/2023-CT read with Notification No. 25/2023-CT dated 17.07.2023.

That window has closed, and its five financial years are now also caught by the three-year bar. It is recorded here because unfiled returns for those years are still encountered, and the applicable fee is the full slab rate, not the capped ₹20,000.

The three-year bar

Section 44(2), inserted by section 144 of the Finance Act, 2023 and notified by Notification No. 28/2023-CT dated 31.07.2023 with effect from 01.10.2023:

"A registered person shall not be allowed to furnish an annual return under sub-section (1) for a financial year after the expiry of a period of three years from the due date of furnishing the said annual return."

With a relief power: "the Government may, on the recommendations of the Council, by notification, and subject to such conditions and restrictions as may be specified therein, allow a registered person or a class of registered persons to furnish an annual return for a financial year… even after the expiry of the said period of three years."

This is a different kind of consequence from a late fee. A fee is a cost of delay; the bar is an extinction of the ability to comply. A taxpayer past three years cannot file, cannot self-correct under section 73, and is left with whatever the department assesses.

The clock runs from the due date, not from the year end. For a financial year ending 31 March with a 31 December due date, the bar falls on 31 December three years later — nine months longer than a year-end measure would give.

The other consequences of not filing

Notice to defaulters — section 46. "where a registered person fails to furnish a return under section 39 or section 44 or section 45, a notice shall be issued requiring him to furnish such return within fifteen days."

General penalty — section 125. "any person, who contravenes any of the provisions of this Act or any rules made thereunder for which no penalty is separately provided, shall be liable to a penalty which may extend to ₹25,000" — with an equal amount under the SGST/UTGST Act, so up to ₹50,000.

But the Guide is careful about how section 125 may be applied:

"It is important to note that to impose a penalty under section 125 up to ₹25,000, the ingredients such as wilful default, etc., must be established by a process of adjudication allowing a reasonable opportunity to the taxable person and not imposed as a matter of routine."

That is a real limitation. Section 125 is a residual penalty requiring adjudication and an opportunity of hearing — it is not an automatic add-on to a late fee.

Why a due date exists at all

The Guide makes an observation worth keeping in view when assessing exposure:

"Annual return has a due date prescribed for its filing. However, there is no embargo on filing this return belatedly. Due date prescribed… is necessary to make this return enforceable. Without a due date, this return would become directory and not mandatory given that taxes due are paid through monthly/quarterly return in Form GSTR-3B."

And: "Annual return is also not a document wherein new information can be furnished. Instead, Form GSTR-9 only curates the information already furnished through the return in Form GSTR-1 or Form GSTR-3B and presents it in a suitable manner for consideration by the tax administration."

Two consequences follow from that characterisation. The revenue impact of late filing is presentational rather than fiscal — the tax was already paid through GSTR-3B — which is why the sanction is a fee rather than interest. And it explains why section 44(2)'s bar is tolerable at all: nothing is lost to the exchequer by a return that can no longer be filed. What is lost is the taxpayer's own self-correction opportunity under section 73. GSTR-9 and DRC-03 →

Key takeaways

• Section 47(2): ₹100 per day, capped at 0.25% of turnover in the State or UT — mirrored under SGST/UTGST.
• Notification No. 07/2023-CT created three slabs from FY 2022-23: ₹25/day at 0.02%, ₹50/day at 0.02%, ₹100/day at 0.25%, for turnover up to ₹5 crore, ₹5–20 crore, and above ₹20 crore.
• The cap moves far more than the daily rate across slabs — from 0.02% to 0.25%.
• The ₹20,000 amnesty for FY 2017-18 to 2021-22 expired on 31 August 2023.
• Section 44(2), from 01.10.2023, bars filing three years after the due date — with a Government power to relax on the Council's recommendation.
• The bar runs from the due date, not from the year end.
• Section 46 allows a notice requiring the return within fifteen days; section 125 allows up to ₹25,000 + ₹25,000, but only on adjudication establishing wilful default.
• Late filing costs a fee, not interest, because GSTR-9 curates information already filed rather than carrying new tax.

Read next

• GSTR-9: Who Must File, and Who Is Exempt
• GSTR-9: Primary Data Source — GSTR-1, GSTR-3B or Books?
• Section 47: Late Fee Caps and Nil Return Filing

Disclaimer: Positions stated as on 5 September 2026, based on sections 44, 46, 47(2) and 125 of the CGST Act, 2017, section 144 of the Finance Act, 2023, and Notifications No. 07/2023, 25/2023 and 28/2023-Central Tax, as reproduced in the ICAI Technical Guide on GST Annual Return (Form GSTR-9).